Adding Ontology.getParents().

Fixes: #18
Phenomics · Sep 4, 2017 · 808c1bd · 808c1bd
1 parent ed4e478
commit 808c1bd
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diff --git a/ontolib-core/src/main/java/com/github/phenomics/ontolib/ontology/data/Ontology.java b/ontolib-core/src/main/java/com/github/phenomics/ontolib/ontology/data/Ontology.java
@@ -2,6 +2,8 @@
 
 import java.io.Serializable;
 import java.util.Collection;
+import java.util.HashSet;
+import java.util.Iterator;
 import java.util.Set;
 
 /**
@@ -17,15 +19,17 @@
  * @author <a href="mailto:[email protected]">Manuel Holtgrewe</a>
  * @author <a href="mailto:[email protected]">Sebastian Koehler</a>
  */
-public interface Ontology<T extends Term,
-    R extends TermRelation> extends MinimalOntology<T, R>, Serializable {
+public interface Ontology<T extends Term, R extends TermRelation>
+    extends
+      MinimalOntology<T, R>,
+      Serializable {
 
   /**
    * Translate {@link TermId} to primary one (in case of alternative or deprecated term IDs).
    *
    * @param termId The {@link TermId} to translate.
-   * @return Primary {@link TermId} (might be the same as <code>termId</code>), <code>null</code>
-   *         if none could be found.
+   * @return Primary {@link TermId} (might be the same as <code>termId</code>), <code>null</code> if
+   *         none could be found.
    */
   default TermId getPrimaryTermId(TermId termId) {
     final Term term = getTermMap().get(termId);
@@ -78,13 +82,28 @@ default Set<TermId> getAllAncestorTermIds(Collection<TermId> termIds) {
     return getAllAncestorTermIds(termIds, true);
   }
 
+  /**
+   * Return the {@link TermId}s of the parents of {@code termId}.
+   *
+   * @param termId The ID of the term to query the parents for.
+   * @return The resulting parent {@link TermId}s of {@code termId}.
+   */
+  default Set<TermId> getParentTermIds(TermId termId) {
+    final Set<TermId> result = new HashSet<>();
+    final Iterator<TermId> it = getGraph().viaOutEdgeIterator(termId);
+    while (it.hasNext()) {
+      result.add(it.next());
+    }
+    return result;
+  }
+
   /**
    * Construct and return sub ontology, starting from {@code subOntologyRoot}.
    *
    * <h5>Sub Ontology Iteration Remark</h5>
    *
    * <p>
-   * The constructed sub ontology will use the same maps from {@link TermId} to {@link T} and same
+   * The constructed sub ontology will use the same maps from {@link TermId} to {@code T} and same
    * edge relation maps as the original ontology. However, the functions
    * {@link Ontology#getAllTermIds()}, {@link Ontology#getNonObsoleteTermIds()},
    * {@link Ontology#getObsoleteTermIds()}, and {@link Ontology#getTerms()} will only contain the

diff --git a/...-core/src/test/java/com/github/phenomics/ontolib/ontology/data/ImmutableOntologyTest.java b/...-core/src/test/java/com/github/phenomics/ontolib/ontology/data/ImmutableOntologyTest.java
@@ -31,6 +31,9 @@ public void test() {
         "[ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000001], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000002], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000003], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000004], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000005]]",
         ontology.getNonObsoleteTermIds().toString());
     assertEquals("[]", ontology.getObsoleteTermIds().toString());
+    assertEquals(
+        "[ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000002], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000003], ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000004]]",
+        ontology.getParentTermIds(id1).toString());
   }
 
 }